Publications in Journals:
V. Acuña, Etienne Birmelé, L. Cottret, P. Crescenzi, F. Jourdan, V. Lacroix, A. Marchetti-Spaccamela, A. Marino, P. V. Milreu, M.-F. Sagot, L. Stougie, Telling Stories in Metabolic Networks, Theoretical Computer Science Volume 457, Pages 1-9, 2012.
V. Acuña, L. Cottret, P. V. Milreu, A. Marchetti-Spaccamela, L. Stougie, M.-F. Sagot, Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks, Oxford Bioinformatics Volume 28, Issue 19, Pages 2474-2483, 2012.
V. Acuña, C. E. Ferreira, A. S. Freire, E. Moreno, Solving the maximum edge biclique packing problem on unbalanced bipartite graphs, Disc. App. Math. In Press, 2011.
L. Cottret, P. V. Milreu, V. Acuña, A. Marchetti-Spaccamela, L. Stougie, H. Charles, M.-F. Sagot, Graph based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata, PLoS Comput. Biol. 6(9), 2010.
V. Acuña, A. Marchetti-Spaccamela, M.-F. Sagot, L. Stougie. A note on the complexity of finding and enumerating elementary modes. Biosystems, 99(3):210-214, 2010.
V. Acuña, F. Chierichetti, V. Lacroix, A. Marchetti-Spaccamela, M.-F. Sagot, and L. Stougie. Modes and cuts in metabolic networks: Complexity and algorithms. BioSystems, 95(1):51-50, 2008.
V. Acuña, G. Didier, A. Maass, Coding with variable block maps, Theoretical Computer Science, 369(1-3):396-405, 2006.
Extended abstracts:
L. Cottret, P. V. Milreu, V. Acuña, A. Marchetti-Spaccamela, F. V. Martinez, M.-F. Sagot and L. Stougie. Enumerating precusor sets of metabolites in a metabolic network. WABI'08, Lecture Notes in Computer Science/Lecture Notes in BioInformatics, volume 5251, pages 233-244, 2008.
P. Milreu, V. Acuña, E. Birmelé, P. Crescenzi, A. Marchetti-Spaccamela, M. Sagot, L. Stougie and V. Lacroix, Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms, WABI 2010, Lecture Notes in Computer Science, Springer, 2010.
V. Acuña, C. E. Ferreira, A. S. Freire, E. Moreno, The biclique k-clustering problem in bipartite graphs and its application in bioinformatics. Proceedings of ISCO, 2010. International Symposium on Combinatorial Optimization, 2010.
L. Cottret, P. V. Milreu, V. Acuña, A. Marchetti-Spaccamela, F. V. Martinez, M. F Sagot, L. Stougie, Enumerating Precursor Sets of Target Metabolites in a Metabolic Network. WABI 2008, Lecture Notes in Computer Science, 5251: 233-244 Springer, 2008.
Other Publications:
V. Acuña, Models and algorithms for metabolic networks: elementary modes and precursor sets. PhD Thesis. Université Claude Bernard Lyon 1. June, 2010.
L. Cottret, V. Acuña, H. Charles, M. F. Sagot, Recherche de précurseurs dans un réseau métabolique, (in french). Riams07, edited by J. P. Comet, F. Quessette and S. Vial, 2007.
V. Acuña, C-writing and Classification by Context, (in spanish), Thesis of M.Sc. In Computer Science, Universidad de Chile, 2004.